[Chimera-users] Calculation of RMSD between 2 PDB structures automatically

Sumitro Harjanto u0601918 at nus.edu.sg
Wed Oct 21 04:46:16 PDT 2009



I have about 150 peptide structures in PDB format. I would like to
compare each of them with a Template Structure (also in PDB format) and
obtain an RMSD measurement for each comparison. 


These peptides are similar in structures to the template but may have
very low sequence similarity/conservation.


So my question is:

1.	what is the command I should use given this scenario..? I was
quite confused with the many different commands such as: rmsd, match,
ensemblematch, matchmaker,... can anyone enlighten me on the differences
among them. I would like to find one which can align/superimpose 2
peptides and calculate RMSD (Ca or backbone)


2.	Is there a way to automate the process through scripting..?


I'm still young with CHIMERA so please pardon my ignorance. =]




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